[Bioclusters] (no subject)

LAI Loong Fong bioclusters@bioinformatics.org
Wed, 31 Mar 2004 09:11:46 +0600

On our Tru64 boxes, we usually turn off vm_swap_eager to make is do 
lazy swap. It depend on what you wanted to achieve. As Tru64 is running 
on the Alpha which is a truly 64 bit OS and CPU, having more swap is 
better than less as your processes can really use up whatever memory 
you can put into your box. I have blast and ssaha jobs using ~20GB of 

LAI Loong-Fong

On Mar 31, 2004, at 1:27 AM, Tim Cutts wrote:

> On 30 Mar 2004, at 19:00, Dan Bolser wrote:
>> On Wed, 31 Mar 2004, LAI Loong Fong wrote:
>>> Hmm strange that you are getting 2GB per process, my large job 
>>> normally
>>> died around the 3GB on a standard linux kernel. Size of swap got
>>> nothing to do with this limit especially when you already has 4GB of
>> This was just a rumour I heard about true64. Kernel limits physical 
>> memory
>> to the size of the swap for some reason.
> I think you are referring to Tru64's two methods of swap allocation.  
> There is a kernel tunable parameter in Tru64 called vm_swap_eager.  
> This can be set to one of two modes.
> As I understand it, it works like this:
> Most programs allocate far more memory than they use.  This can cause 
> problems, so most operating systems overcommit memory and swap.  The 
> problem with this approach is that if you malloc a lot of memory, the 
> malloc may succeed, but when you later try to use it, the OS cannot 
> fulfil its promises, and really nasty things happen.
> Tru64 can operate in this way, just like other operating systems (and 
> is the way we have it set).  But it might be set to its alternative 
> mode, whereby malloc actually immediately allocates from swap.  If 
> there isn't sufficient swap available, the malloc fails immediately.  
> In this mode, memory allocated is *guaranteed* to be available to the 
> application, which for certain applications can make things more 
> reliable.  The machine will never run out of memory at a time other 
> than at the point of memory allocation.
> I seem to remember that IRIX has a similar tunable parameter for 
> memory use.
> Tim
> -- 
> Dr Tim Cutts
> Informatics Systems Group
> Wellcome Trust Sanger Institute
> Hinxton, Cambridge, CB10 1SA, UK
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